Re: [AMBER-Developers] hydrogen mass repartitioning

From: Adrian Roitberg <>
Date: Wed, 12 Mar 2014 11:34:56 -0400

Hi all

Please try it out! Make sure to use the proper scripts to get the new
masses, do not just increase time step to 4 fs !

We are writing a paper on this and will share it with everyone when we
have a good draft.


On 3/12/14 9:55 AM, Thomas Cheatham wrote:
>>> Note AMBER 14 will also support hydrogen mass
>>> repartitioning so in principal you can run at 4fs time step.
>> How much to we really know about this option? I've been playing with it for
> We have been running a DNA 18-mer and also a RNA tetranucleotide r(GACC)
> with h-mass repartitioning on the solute only and on everything. From
> initial analysis, conformational distributions appear fairly identical for
> the r(GACC), however we still need to look at kinetics, water properties
> (viscosity should be higher), etc. When Christina, Ros and I get it
> further analyzed, I'll summarize to the dev list...
>> Blue Waters (say) to run lots of simulations at 1, 2 and 4 fs time steps?
>> Has anyone compared 2 and 4 fs where both have the mass repartitioning?
> Ros/Christina, maybe we should fire up some more as per above. --tom
> _______________________________________________
> AMBER-Developers mailing list

                             Dr. Adrian E. Roitberg
Colonel Allan R. and Margaret G. Crow Term Professor.
Quantum Theory Project, Department of Chemistry
University of Florida
AMBER-Developers mailing list
Received on Wed Mar 12 2014 - 09:00:02 PDT
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